Structure of PDB 4ub5 Chain A

Receptor sequence

>4ub5A (length=310) Species: 9606 (Homo sapiens) [Search protein sequence]

TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEA
KKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPS
AARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQ
DIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESKLLHQ
VVEQLQKVHFITDTLSKGETKFMGVCQLPSEYPHRRIDIRLIPKDQYYCG
VLYFTGSDIFNKNMRAHALEKGFTINEYTIRPGEPLPVDSEKDIFDYIQW
KYREPKDRSE

3D structure

PDB

4ub5 Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.

Chain

Resolution

2.15 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	D190 D192 D256
Catalytic site (residue number reindexed from 1)	D181 D183 D238
Enzyme Commision number	2.7.7.7: DNA-directed DNA polymerase. 4.2.99.- 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)
BS01	dna	A	H34 S229 K230 G231 T233 K234 R258 R283 T292 I293 N294 E295 Y296	H25 S216 K217 G218 T220 K221 R240 R265 T274 I275 N276 E277 Y278
BS02	dna	A	S104 G105 G107 P108 S109 A110 R254 D256 Y271	S95 G96 G98 P99 S100 A101 R236 D238 Y253
BS03	dna	A	K35 A38 G64 V65 G66 K68 I69	K26 A29 G55 V56 G57 K59 I60
BS04	MN	A	D190 D192 D256	D181 D183 D238
BS05	MN	A	D190 D192	D181 D183
BS06	8DG	A	G179 S180 S188 G189 D190 D192 Y271 F272 T273 G274 D276 N279 R283	G170 S171 S179 G180 D181 D183 Y253 F254 T255 G256 D258 N261 R265

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0003684	damaged DNA binding
GO:0003887	DNA-directed DNA polymerase activity
GO:0003906	DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0005515	protein binding
GO:0008017	microtubule binding
GO:0016779	nucleotidyltransferase activity
GO:0016829	lyase activity
GO:0019899	enzyme binding
GO:0034061	DNA polymerase activity
GO:0046872	metal ion binding
GO:0051575	5'-deoxyribose-5-phosphate lyase activity
GO:0140078	class I DNA-(apurinic or apyrimidinic site) endonuclease activity

	Biological Process
GO:0001701	in utero embryonic development
GO:0006259	DNA metabolic process
GO:0006260	DNA replication
GO:0006261	DNA-templated DNA replication
GO:0006281	DNA repair
GO:0006284	base-excision repair
GO:0006287	base-excision repair, gap-filling
GO:0006290	pyrimidine dimer repair
GO:0006297	nucleotide-excision repair, DNA gap filling
GO:0006303	double-strand break repair via nonhomologous end joining
GO:0006915	apoptotic process
GO:0006954	inflammatory response
GO:0006974	DNA damage response
GO:0007435	salivary gland morphogenesis
GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage
GO:0010332	response to gamma radiation
GO:0016445	somatic diversification of immunoglobulins
GO:0016446	somatic hypermutation of immunoglobulin genes
GO:0045471	response to ethanol
GO:0048535	lymph node development
GO:0048536	spleen development
GO:0048872	homeostasis of number of cells
GO:0051402	neuron apoptotic process
GO:0055093	response to hyperoxia
GO:0071707	immunoglobulin heavy chain V-D-J recombination
GO:0071897	DNA biosynthetic process

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005874	microtubule
GO:0005876	spindle microtubule
GO:0032991	protein-containing complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:4ub5, PDBe:4ub5, PDBj:4ub5
PDBsum	4ub5
PubMed	25409153
UniProt	P06746\|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)

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